User

Overview

The ali2d_c (original version) is for performing 2-D reference-free alignment of an image series (without CTF correction). For the optimization purpose, the optimized ali2d cm (modified version) dosen't have x range (sx) and y range (sy) which are for translation search in x and y directions. We also ignore the translation step in this case since we don't have any search direction.

Develop Environment

Python

Python is a dynamic object-oriented programming language that offers strong support for integration with C++, comes with extensive libraries running on Linux/Unix.

SPARX

EMAN2

EMAN2' is focus on providing single particle reconstruction methods. EMAN consists of C++ library with bindings to the Python programming language. SPARX also relies on the EMAN2 library of fundamental C++ image processing functions.

Before you start programming

Installation

The 'SPARX' packages are installed under a user-chosen directory. Installation from source is fully compatible with your system. After download the source, the steps are

Upload individual parts to CVS

Remove individual parts to CVS

To run Python program

There are two ways to start running Pyton code. First, you can simply type the command on the window sparx and it allows your computer start the sparx console. To use SPARX library, you need to import fuctions first.

In [1]: from sparx import *

If you want to test one specific function, for example info, in applications.py located in /user/home/sparx/lipbin, then you type on the console like below,

In [2]: from applications import info
In [3]: info(''file or parameter name'')

Of course, you don't want to type every single line command on the console. To make an excute pyton file, we need to put below code inside of the file. Make sure that your_python_program has to be same as the file name.